Methods for analyzing nucleic acids by isolating and amplifying nucleic acid sequences in vitro are widely known and used in research, forensics, medicine and agriculture. One of the best-known amplification methods is the polymerase chain reaction (PCR), which is a target amplification method. The development of isothermal nucleic acid target amplification technologies circumvents the need for expensive instrumented thermal cyclers required for PCR. Such methods include, but are not limited to, the Recombinase Polymerase Amplification (RPA) method (see for example U.S. Pat. No. 7,485,428); Strand Displacement Amplification (SDA), (See for example, U.S. Pat. Nos. 5,455,166 and 5,470,723); Transcription-Mediated Amplification (TMA), (See for example, Guatelli eta., Proc. Natl. Acad. Sci. USA 87:1874-1878 (1990)); Rolling Circle Amplification (RCA), (See for example, Fire and Xu, Proc. Natl. Acad Sci. USA 92:4641-4645 (1995); Lui, et al., J. Am. Chem. Soc. 118:1587-1594 (1996); Lizardi, et al., Nature Genetics 19:225-232 (1998), U.S. Pat. Nos. 5,714,320 and 6,235,502); Helicase Dependant Amplification (HDA), (see for example Vincent et al., EMBO Reports 5(8): 795-800 (2004); U.S. Pat. No. 7,282,328); and Multiple Displacement Amplification (MDA) (See for example Dean et. al., Proc. Natl. Acad Sci. USA 99:5261-5266 (2002)).
Although nucleic acid amplification and detection technologies have improved, the current methods still perpetuate the basic paradigm of performing the main steps (nucleic acid isolation, amplification, and detection or analysis) in vitro, in a reaction tube or vessel. In vitro analysis first requires steps to acquire a sample of the target material, for example tissue or cells before performing nucleic acid isolation, amplification, and detection steps. In high throughput situations where numerous samples are needed, the sampling process can become a time, labor, or ergonomic burden, not to mention increasing the use of consumable laboratory supplies and the possibility of error due to cross contamination with other samples, or a mix-up in sample identification. In other situations, laboratory facilities and/or equipment may not be readily available, for example where it is impossible, impractical, or undesirable to move or remove samples or specimens from their current environment. In other situations, sample destruction may be undesirable, such as in the case of museum artifact or specimen testing. Worse, in other situations involving live animal subjects, obtaining a sample can be invasive and/or painful. Therefore, a method in which isolation, amplification, and detection or analysis of nucleic acids are performed without the need for sampling or processing target tissue or cells in a closed system or reaction well is desirable.